Bottom Line:
Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276.Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site.The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined.

Affiliation: Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

ABSTRACTIdentifying the targets of broadly neutralizing antibodies to HIV-1 and understanding how these antibodies develop remain important goals in the quest to rationally develop an HIV-1 vaccine. We previously identified a participant in the CAPRISA Acute Infection Cohort (CAP257) whose plasma neutralized 84% of heterologous viruses. In this study we showed that breadth in CAP257 was largely due to the sequential, transient appearance of three distinct broadly neutralizing antibody specificities spanning the first 4.5 years of infection. The first specificity targeted an epitope in the V2 region of gp120 that was also recognized by strain-specific antibodies 7 weeks earlier. Specificity for the autologous virus was determined largely by a rare N167 antigenic variant of V2, with viral escape to the more common D167 immunotype coinciding with the development of the first wave of broadly neutralizing antibodies. Escape from these broadly neutralizing V2 antibodies through deletion of the glycan at N160 was associated with exposure of an epitope in the CD4 binding site that became the target for a second wave of broadly neutralizing antibodies. Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276. Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site. The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined. Altogether this study showed that the human immune system is capable of generating multiple broadly neutralizing antibodies in response to a constantly evolving viral population that exposes new targets as a consequence of escape from earlier neutralizing antibodies.

ppat-1003738-g010: Summary of the role of CAP257 viral evolution in shaping broadly neutralizing antibody responses.The schema depicts the evolution of plasma neutralizing antibodies and viral escape mutations over 240 weeks. Each of the three waves of CAP257 broadly neutralizing antibodies is shown. Text boxes highlight the key events described herein. Env trimers (EMD-5447) were drawn in UCSF-Chimera, and spheres were used to approximate the location of escape mutations. 1) Strain-specific antibodies (dotted orange line) developed at 23 weeks, targeting a V2 epitope overlapping with known V2 antibodies (eg: PG9). 2) Strain-specific V2 antibodies were escaped by an N167D mutation (D being the global consensus at this site). 3) Broadly neutralizing antibodies targeting V2 (wave 1 – red curve) developed at 30 weeks. 4) Escape from wave 1 antibodies through deletion of the N160 glycan was associated with exposure of an epitope in the CD4bs. 5) At 67 weeks broadly neutralizing antibodies targeting the CD4bs (wave 2 – green curve) develop. Neutralization was N276 glycan dependent and sensitive to an N279D mutation. 6) The N279D change emerges at 93 weeks, significantly affecting wave 2 neutralization at this time point. 7) Wave 2 neutralization becomes independent of position 279, which was associated with increased neutralization breadth. 8) Mutations that delete the N276 glycan (as well as an R456W change) escape wave 2 antibodies. 9) CAP257 develops a third broadly neutralizing antibody specificity that could not be mapped to any of the four known antibody targets.

Mentions:
A preventative HIV-1 vaccine remains the most likely way to end the HIV pandemic, but current envelope immunogens have so far failed to elicit broadly neutralizing antibodies. Nonetheless, the development of cross-reactive antibodies in approximately a quarter of HIV-1 infected individuals has confirmed that the human immune system can make such antibodies. Much emphasis has been placed on mapping the targets for these broadly neutralizing antibodies in an attempt to define viral vulnerabilities for immunogen design. Here we analyzed CAP257 heterologous neutralization over a 4.5 year period, describing the sequential evolution of three distinct broadly neutralizing antibody specificities within a single HIV-1 subtype C infected individual. We further showed how early viral evolution in the context of broadly reactive antibodies may profoundly shape the maturing antibody response towards enhanced neutralization breadth, in a process that may inform immunogen design. These data have been summarized in Figure 10.

ppat-1003738-g010: Summary of the role of CAP257 viral evolution in shaping broadly neutralizing antibody responses.The schema depicts the evolution of plasma neutralizing antibodies and viral escape mutations over 240 weeks. Each of the three waves of CAP257 broadly neutralizing antibodies is shown. Text boxes highlight the key events described herein. Env trimers (EMD-5447) were drawn in UCSF-Chimera, and spheres were used to approximate the location of escape mutations. 1) Strain-specific antibodies (dotted orange line) developed at 23 weeks, targeting a V2 epitope overlapping with known V2 antibodies (eg: PG9). 2) Strain-specific V2 antibodies were escaped by an N167D mutation (D being the global consensus at this site). 3) Broadly neutralizing antibodies targeting V2 (wave 1 – red curve) developed at 30 weeks. 4) Escape from wave 1 antibodies through deletion of the N160 glycan was associated with exposure of an epitope in the CD4bs. 5) At 67 weeks broadly neutralizing antibodies targeting the CD4bs (wave 2 – green curve) develop. Neutralization was N276 glycan dependent and sensitive to an N279D mutation. 6) The N279D change emerges at 93 weeks, significantly affecting wave 2 neutralization at this time point. 7) Wave 2 neutralization becomes independent of position 279, which was associated with increased neutralization breadth. 8) Mutations that delete the N276 glycan (as well as an R456W change) escape wave 2 antibodies. 9) CAP257 develops a third broadly neutralizing antibody specificity that could not be mapped to any of the four known antibody targets.

Mentions:
A preventative HIV-1 vaccine remains the most likely way to end the HIV pandemic, but current envelope immunogens have so far failed to elicit broadly neutralizing antibodies. Nonetheless, the development of cross-reactive antibodies in approximately a quarter of HIV-1 infected individuals has confirmed that the human immune system can make such antibodies. Much emphasis has been placed on mapping the targets for these broadly neutralizing antibodies in an attempt to define viral vulnerabilities for immunogen design. Here we analyzed CAP257 heterologous neutralization over a 4.5 year period, describing the sequential evolution of three distinct broadly neutralizing antibody specificities within a single HIV-1 subtype C infected individual. We further showed how early viral evolution in the context of broadly reactive antibodies may profoundly shape the maturing antibody response towards enhanced neutralization breadth, in a process that may inform immunogen design. These data have been summarized in Figure 10.

Bottom Line:
Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276.Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site.The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined.

Affiliation:
Centre for HIV and STIs, National Institute for Communicable Diseases (NICD), of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

ABSTRACTIdentifying the targets of broadly neutralizing antibodies to HIV-1 and understanding how these antibodies develop remain important goals in the quest to rationally develop an HIV-1 vaccine. We previously identified a participant in the CAPRISA Acute Infection Cohort (CAP257) whose plasma neutralized 84% of heterologous viruses. In this study we showed that breadth in CAP257 was largely due to the sequential, transient appearance of three distinct broadly neutralizing antibody specificities spanning the first 4.5 years of infection. The first specificity targeted an epitope in the V2 region of gp120 that was also recognized by strain-specific antibodies 7 weeks earlier. Specificity for the autologous virus was determined largely by a rare N167 antigenic variant of V2, with viral escape to the more common D167 immunotype coinciding with the development of the first wave of broadly neutralizing antibodies. Escape from these broadly neutralizing V2 antibodies through deletion of the glycan at N160 was associated with exposure of an epitope in the CD4 binding site that became the target for a second wave of broadly neutralizing antibodies. Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276. Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site. The third wave targeted a quaternary epitope that did not overlap any of the four known sites of vulnerability on the HIV-1 envelope and remains undefined. Altogether this study showed that the human immune system is capable of generating multiple broadly neutralizing antibodies in response to a constantly evolving viral population that exposes new targets as a consequence of escape from earlier neutralizing antibodies.